org.jmol.jvxl.readers
Class VolumeFileReader

java.lang.Object
  extended by org.jmol.jvxl.readers.VoxelReader
      extended by org.jmol.jvxl.readers.VolumeFileReader
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
ApbsReader, CubeReader, JaguarReader, JvxlReader, PltFormattedReader, XplorReader

 class VolumeFileReader
extends VoxelReader


Field Summary
protected  int atomCount
           
protected  java.io.BufferedReader br
           
protected  boolean canDownsample
           
private  int[] downsampleRemainders
           
protected  boolean endOfData
           
protected  boolean isAngstroms
           
(package private)  java.lang.String line
           
protected  boolean negativeAtomCount
           
(package private)  int[] next
           
private  int nSurfaces
           
 
Fields inherited from class org.jmol.jvxl.readers.VoxelReader
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultColorFractionBase, defaultColorFractionRange, defaultCutoff, defaultEdgeFractionBase, defaultEdgeFractionRange, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, fReturn, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData
 
Constructor Summary
VolumeFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
private  int countData(java.lang.String str)
           
(package private) static java.lang.String determineFileType(java.io.BufferedReader bufferedReader)
           
(package private)  void discardTempData(boolean discardAll)
           
protected  float getNextVoxelValue(java.lang.StringBuffer sb)
           
(package private)  java.lang.String[] getTokens()
           
protected  void gotoData(int n, int nPoints)
           
protected  float nextVoxel()
           
(package private)  float parseFloat()
           
(package private)  float parseFloat(java.lang.String s)
           
(package private)  float parseFloatNext(java.lang.String s)
           
(package private)  int parseInt()
           
(package private)  int parseInt(java.lang.String s)
           
(package private)  int parseInt(java.lang.String s, int iStart)
           
(package private)  int parseIntNext(java.lang.String s)
           
protected  void readAtomCountAndOrigin()
           
protected  int readExtraLine()
           
protected  void readTitleLines()
           
(package private)  void readVolumeData(boolean isMapData)
           
(package private)  void readVolumeParameters()
           
protected  int readVolumetricHeader()
           
protected  void readVoxelData(boolean isMapData)
           
protected  void readVoxelVector(int voxelVectorIndex)
           
protected  int skipComments(boolean addToHeader)
           
private  void skipData(int nPoints)
           
private  void skipVoxels(int n)
           
 
Methods inherited from class org.jmol.jvxl.readers.VoxelReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getCalcPoint, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointIndex, gotoAndReadVoxelData, initializeVolumetricData, isInside, jvxlUpdateInfo, readColorData, readSurfacePoint, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

br

protected java.io.BufferedReader br

endOfData

protected boolean endOfData

negativeAtomCount

protected boolean negativeAtomCount

atomCount

protected int atomCount

nSurfaces

private int nSurfaces

isAngstroms

protected boolean isAngstroms

canDownsample

protected boolean canDownsample

downsampleRemainders

private int[] downsampleRemainders

line

java.lang.String line

next

int[] next
Constructor Detail

VolumeFileReader

VolumeFileReader(SurfaceGenerator sg,
                 java.io.BufferedReader br)
Method Detail

determineFileType

static java.lang.String determineFileType(java.io.BufferedReader bufferedReader)

discardTempData

void discardTempData(boolean discardAll)
Overrides:
discardTempData in class VoxelReader

readVolumeParameters

void readVolumeParameters()
Specified by:
readVolumeParameters in class VoxelReader

readVolumeData

void readVolumeData(boolean isMapData)
Specified by:
readVolumeData in class VoxelReader

readVolumetricHeader

protected int readVolumetricHeader()

readTitleLines

protected void readTitleLines()
                       throws java.lang.Exception
Throws:
java.lang.Exception

skipComments

protected int skipComments(boolean addToHeader)
                    throws java.lang.Exception
Throws:
java.lang.Exception

readAtomCountAndOrigin

protected void readAtomCountAndOrigin()
                               throws java.lang.Exception
Throws:
java.lang.Exception

readVoxelVector

protected void readVoxelVector(int voxelVectorIndex)
                        throws java.lang.Exception
Throws:
java.lang.Exception

readExtraLine

protected int readExtraLine()
                     throws java.lang.Exception
Throws:
java.lang.Exception

readVoxelData

protected void readVoxelData(boolean isMapData)
                      throws java.lang.Exception
Specified by:
readVoxelData in class VoxelReader
Throws:
java.lang.Exception

skipVoxels

private void skipVoxels(int n)
                 throws java.lang.Exception
Throws:
java.lang.Exception

getNextVoxelValue

protected float getNextVoxelValue(java.lang.StringBuffer sb)
                           throws java.lang.Exception
Throws:
java.lang.Exception

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception
Throws:
java.lang.Exception

gotoData

protected void gotoData(int n,
                        int nPoints)
                 throws java.lang.Exception
Overrides:
gotoData in class VoxelReader
Throws:
java.lang.Exception

skipData

private void skipData(int nPoints)
               throws java.lang.Exception
Throws:
java.lang.Exception

countData

private int countData(java.lang.String str)

getTokens

java.lang.String[] getTokens()

parseFloat

float parseFloat()

parseFloat

float parseFloat(java.lang.String s)

parseFloatNext

float parseFloatNext(java.lang.String s)

parseInt

int parseInt()

parseInt

int parseInt(java.lang.String s)

parseIntNext

int parseIntNext(java.lang.String s)

parseInt

int parseInt(java.lang.String s,
             int iStart)